EasyMetagenome: A user‐friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research

• DOI: 10.1002/imt2.70001
• Publication Date: 2025-02-14T14:35:56Z
• Authors: Defeng Bai; Tong Chen; Jiani Xun; Chuang Ma; Hao Luo; Haifei Yang; Chen Cao; Xiaofeng Cao; Jianzhou Cui; Yuan‐Ping Deng; Zhaochao Deng; Wenxin Dong; Wenxue Dong; Juan Du; Qunkai Fang; Wei Fang; Yue Fang; Fangtian Fu; Min Fu; Yi‐Tian Fu; He Gao; Jingping Ge; Qinglong Gong; Lunda Gu; Peng Guo; Yuhao Guo; Tang Hai; Hao Liu; Jieqiang He; Zi‐Yang He; Huiyu Hou; Can Huang; Shuai Ji; ChangHai Jiang; Gui‐Lai Jiang; Lingjuan Jiang; Ling N. Jin; Yuhe Kan; Da Kang; Jin Kou; Ka‐Lung Lam; Changchao Li; Chong Li; Fuyi Li; Liwei Li; Miao Li; Xin Li; Ye Li; Zheng‐Tao Li; Jing Liang; Yongxin Lin; Changzhen Liu; Danni Liu; Fengqin Liu; Jia Liu; Tianrui Liu; Tingting Liu; Xinyuan Liu; Yaqun Liu; Bangyan Liu; Minghao Liu; Wenbo Lou; Yaning Luan; Yuanyuan Luo; Hujie Lv; Tengfei Ma; Zongjiong Mai; Jiayuan Mo; Dongze Niu; Zhuo Pan; Heyuan Qi; Zhanyao Shi; Chunjiao Song; Fuxiang Sun; Yan Sun; Sihui Tian; Xiulin Wan; Guoliang Wang; Hongyang Wang; Hongyu Wang; Huanhuan Wang; Jing Wang; Jun Wang; Kang Wang; Leli Wang; Shao‐kun Wang; Xinlong Wang; Yao Wang; Zufei Xiao; Huichun Xing; Yifan Xu; Shu‐yan Yan; Li Yang; Song Yang; Yuanming Yang; Xiaofang Yao; Salsabeel Yousuf; Hao Yu; Yu Lei; Zhengrong Yuan; Meiyin Zeng; Chunfang Zhang; Chunge Zhang; Huimin Zhang; Jing Zhang; Na Zhang; Tianyuan Zhang; Yi‐Bo Zhang; Yupeng Zhang; Zheng Zhang; Mingda Zhou; Yuanping Zhou; Chengshuai Zhu; Lin Zhu; Yue Zhu; Zhihao Zhu; Hongqin Zou; Anna Zuo; Wenxuan Dong; Tao Wen; Shifu Chen; Guoliang Li; Yunyun Gao; Yong‐Xin Liu
• Keywords: Adaptability

Abstract Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in‐depth analysis of microbial communities at both the high‐resolution taxonomic and functional levels. This approach provides valuable insights diversity, interactions, their roles health disease. However, complexity data processing need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, user‐friendly pipeline that supports multiple methods, including quality control host removal, read‐based, assembly‐based, binning, along with advanced genome analysis. The also features customizable settings, comprehensive visualizations, detailed parameter explanations, ensuring its adaptability across wide range scenarios. Looking forward, aim refine by addressing contamination issues, optimizing workflows third‐generation sequencing data, integrating emerging technologies like deep learning network analysis, further enhance accuracy. EasyMetageonome is freely available https://github.com/YongxinLiu/EasyMetagenome .